Just grab the first comment;

$html = '<!--% xxxx UNO xxxx %-->   <!--% xxxx DOS xxxx %-->';
$html =~ s/(<!--.*?-->\s*)<!--%(.*?) DOS (.*?)%-->/$1GONE/s;
print $html;
[download]

Or make sure there is a comment beforehand:

$html = '<!--% xxxx UNO xxxx %-->   <!--% xxxx DOS xxxx %-->';
$html =~ s/-->\s*<!--%(.*?) DOS (.*?)%-->/--> GONE/s;
print $html;
[download]

There is probably a cleaner way to do this without capturing the first comment at all, or by using a g modifier, skipping the first comment and replacing the second.